Yes, clean install for part of softwares will cause this bug.

See Also, https://bugs.launchpad.net/ubuntu/+source/gnome-
panel/+bug/1530555

And the reason is simple, the menu from gnome-panel will display a new
item if a new "desktop" file is created in /usr/share/application/
folder, but the menu will check whether "TryExec=" points to a non-exist
file or an invalid link, if so, the menu still hide this item even after
the target that "TryExec=" points to become valid.

One of the following solutions can fix this bug,

1. force dpkg to postpone installing "[DEB]/usr/share/applications/*"
files in the deb package, in order to make the file that "TryExec="
points to become valid first.

2. add a trigger after every dpkg installation finish to force updating
the whole menus.

3. force gnome-panel to ignore "TryExec=" field to let menu item always
show.

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https://bugs.launchpad.net/bugs/1518775

Title:
  gnome-panel cannot show newly installed software icons

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